{"id":24961660,"url":"https://github.com/esteinig/vircov","last_synced_at":"2025-07-07T01:05:25.909Z","repository":{"id":42676860,"uuid":"468284801","full_name":"esteinig/vircov","owner":"esteinig","description":"Viral genome coverage evaluation for metagenomic diagnostics :drop_of_blood:","archived":false,"fork":false,"pushed_at":"2024-12-10T03:51:49.000Z","size":32260,"stargazers_count":28,"open_issues_count":3,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-10T21:40:27.666Z","etag":null,"topics":["bioinformatics","coverage","diagnostics","metagenomics","minimap2","rust","viral-metagenomics"],"latest_commit_sha":null,"homepage":"","language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/esteinig.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-03-10T09:57:08.000Z","updated_at":"2025-04-01T02:38:34.000Z","dependencies_parsed_at":"2024-05-30T01:11:31.652Z","dependency_job_id":"4d4b3262-5d73-4c62-b590-796049f11b87","html_url":"https://github.com/esteinig/vircov","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/esteinig/vircov","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/esteinig%2Fvircov","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/esteinig%2Fvircov/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/esteinig%2Fvircov/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/esteinig%2Fvircov/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/esteinig","download_url":"https://codeload.github.com/esteinig/vircov/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/esteinig%2Fvircov/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996083,"owners_count":23541399,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","coverage","diagnostics","metagenomics","minimap2","rust","viral-metagenomics"],"created_at":"2025-02-03T08:55:29.680Z","updated_at":"2025-07-07T01:05:25.845Z","avatar_url":"https://github.com/esteinig.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vircov \u003ca href='https://github.com/esteinig'\u003e\u003cimg src='docs/vircov.png' align=\"right\" height=\"200\"/\u003e\u003c/a\u003e\n\n![](https://img.shields.io/badge/version-0.8.0-black.svg)\n\nAutomated coverage statistics, genome recovery and subtyping for metagenomic diagnostics of viral infections from reads or alignments.\n\n## Overview\n\n\n**`v1.0.0`**\n\n- [Install](#install)\n- [Examples](#examples)\n- [Concepts](#concepts)\n- [Etymology](#etymology)\n\n## Install\n\nAnaconda installation with dependencies:\n\n```\nmamba create -n vircov -c esteinig vircov\n```\n\nDependencies for full pipeline from reads:\n\n* `bowtie2` | `minimap2` | `strobealign` \n* `samtools`\n* `ivar` \n\nSource installation without dependencies:\n\n```\ngit clone https://github.com/esteinig/vircov\ncd vircov \u0026\u0026 cargo build --release \n```\n\n## Usage\n\n### Virus detection and whole genome recovery\n\n```\n\n```\n\n### Virus population graphs and genomic neighbor typing\n\n```\n\n```\n\n#### Reference databases and subtyping schemes\n\nWe make automatically updated [subtyping databases]() and parsed genotype annotation schemes available for a range of common viral pathogen, at least where data-sharing arrangements make this possible (e.g. NCBI- but not GISAID™-derived assemblies). Scheme extractions and release updates are checked and if necessary corrected by our bioinformatics team at the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Melbourne.\n\n## Concepts\n\n### Low-abundance infections and coverage assessment for detection from reads\n\nDefinitive viral diagnosis from metagenomic clinical samples can be extremely challenging due to low sequencing depth, large amounts of host reads and low infectious titres.\n\nOne way to distinguish a positive viral diagnosis is to look at alignment coverage against one or multiple reference sequences. When only few reads map to the reference - and genome coverage is low - positive infections often display multiple distinct\nalignment regions, as opposed to reads mapping to a single or few regions on the reference. [De Vries et al. (2021)](https://www.sciencedirect.com/science/article/pii/S1386653221000792) summarize this concept succinctly in this figure (adapted):\n\n![devries](https://user-images.githubusercontent.com/12873366/158775480-447d847e-5b0d-487c-a39a-81bdf428e09d.png)\n\nPositive calls in these cases can be made from coverage plots showing the distinct alignment regions and a minimum threshold on the number of regions is chosen by the authors (\u003e 3). `Vircov` computes the number of distinct alignment regions as part of the genome recovery module.\n\n### Genomic neighbor typing using viral population graphs\n\n```\n\n```\n\n## Etymology\n\nNot a very creative abbreviation of \"virus coverage\" but the little spectacles in the logo are a reference to [Rudolf Virchow](https://en.wikipedia.org/wiki/Rudolf_Virchow). His surname is pronounced like `vircov` if you mumble the terminal `v`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Festeinig%2Fvircov","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Festeinig%2Fvircov","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Festeinig%2Fvircov/lists"}